Contacts of the helix formed by residues 150 - 161 (chain Z) in PDB entry 5V09
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 150 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B C 3.7 9.9 + - - -
101B MN 4.2 0.5 + - - -
78Z ASP* 3.5 7.9 - - - +
82Z LEU* 3.9 11.4 - - + +
85Z LYS* 2.8 42.0 + - + +
147Z ALA* 3.4 9.1 - - - +
149Z TYR* 1.3 82.1 + - - +
151Z ALA* 1.3 64.8 + - - +
152Z ASP* 3.4 18.7 + - + +
153Z ALA* 3.6 10.6 + - - +
154Z GLN 3.7 4.2 + - - -
225Z ALA* 5.9 0.3 - - - +
226Z TYR* 2.3 41.2 + - - -
285Z GLN* 3.2 18.5 + - - +
286Z LEU 5.6 1.1 + - - +
401Z MN 4.3 1.7 + - - -
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Residues in contact with ALA 151 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Z ASP* 3.9 17.7 - - - +
76Z VAL* 4.1 17.3 - - + +
77Z PHE 4.1 0.7 - - - -
78Z ASP* 3.0 39.3 + - - +
147Z ALA* 4.0 9.9 - - - -
149Z TYR 3.6 1.4 + - - -
150Z GLU* 1.3 70.9 - - - +
152Z ASP* 1.3 67.9 + - - +
154Z GLN* 3.2 1.4 + - - +
155Z LEU* 2.9 31.4 + - + +
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Residues in contact with ASP 152 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B MN 2.2 29.9 + - - -
30Z ASP* 4.3 1.2 - - - +
150Z GLU* 3.9 11.7 - - + +
151Z ALA* 1.3 76.8 + - - +
153Z ALA* 1.3 57.5 + - - +
155Z LEU* 3.4 1.5 + - - +
156Z ALA* 2.9 27.6 + - - +
171Z ASP* 2.9 6.0 - - - +
173Z ASP* 3.7 2.3 - - - +
174Z LEU* 3.4 26.4 - - + +
177Z PHE* 3.5 26.9 - - + -
401Z MN 2.1 37.3 + - - -
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Residues in contact with ALA 153 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150Z GLU* 3.6 5.3 + - - +
151Z ALA 3.3 0.4 - - - -
152Z ASP* 1.3 78.9 - - - +
154Z GLN* 1.3 57.8 + - - +
156Z ALA* 3.3 6.1 + - - -
157Z TYR 2.9 23.9 + - - -
177Z PHE* 4.4 10.3 - - + -
285Z GLN* 3.7 39.9 - - + +
286Z LEU 4.9 0.9 - - - +
287Z VAL* 3.5 19.1 - - + +
298Z LEU* 3.4 14.3 - - + +
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Residues in contact with GLN 154 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Z VAL* 4.0 13.2 - - + -
145Z LEU* 3.4 30.0 - - + +
147Z ALA* 3.6 25.4 - - + -
148Z PRO* 3.4 12.3 - - + +
150Z GLU 3.7 1.8 + - - -
151Z ALA 3.2 5.5 + - - +
153Z ALA* 1.3 80.0 - - - +
155Z LEU* 1.3 58.0 + - - +
157Z TYR* 3.2 9.9 + - - +
158Z LEU* 2.9 43.5 + - + +
287Z VAL* 3.3 9.5 - - + +
288Z PHE* 2.8 49.0 + - - +
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Residues in contact with LEU 155 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Z ALA* 3.6 28.7 - - + -
29Z VAL 3.8 12.3 - - - +
30Z ASP* 3.6 36.3 - - + +
76Z VAL* 3.7 23.1 - - + -
151Z ALA* 2.9 27.2 + - + +
152Z ASP* 3.6 3.1 - - - +
154Z GLN* 1.3 73.2 - - - +
156Z ALA* 1.3 67.3 + - - +
158Z LEU* 3.2 5.6 + - - +
159Z ASN* 2.9 24.8 + - - +
167Z ILE* 3.5 26.2 - - + +
174Z LEU* 3.7 17.5 - - + -
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Residues in contact with ALA 156 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152Z ASP 2.9 16.8 + - - +
153Z ALA 3.3 5.8 + - - +
155Z LEU* 1.3 76.4 - - - +
157Z TYR* 1.3 56.9 + - - +
159Z ASN* 3.4 1.6 + - - +
160Z LYS* 2.9 35.7 + - + +
177Z PHE* 3.7 33.2 - - + +
179Z CYS* 3.7 20.5 - - - -
298Z LEU* 3.9 12.3 - - + -
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Residues in contact with TYR 157 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Z ALA 2.9 13.2 + - - +
154Z GLN* 3.5 22.2 - - - +
156Z ALA* 1.3 74.5 - - - +
158Z LEU* 1.3 62.7 + - + +
160Z LYS* 4.7 3.4 - - + -
161Z ALA* 2.8 60.8 + - + +
163Z ILE* 4.6 4.3 - - + +
287Z VAL* 3.8 20.6 - - + -
289Z ASP* 2.9 43.6 + - - -
290Z PRO* 4.1 8.5 - - + -
296Z ILE* 3.5 20.3 - - + +
297Z PRO 5.2 0.2 - - - -
298Z LEU* 3.4 26.4 - - + +
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Residues in contact with LEU 158 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Z ALA* 4.0 13.0 - - + -
74Z ILE* 4.5 10.8 - - + -
76Z VAL* 3.8 29.6 - - + -
145Z LEU* 4.1 9.4 - - + -
154Z GLN* 2.9 34.0 + - - +
155Z LEU* 3.6 7.0 - - - +
157Z TYR* 1.3 79.8 - - + +
159Z ASN* 1.3 57.6 + - - +
161Z ALA* 4.7 0.4 - - - -
162Z GLY 3.6 0.2 + - - -
163Z ILE* 3.0 42.7 + - + -
164Z VAL* 3.0 37.1 + - + -
290Z PRO* 4.0 13.5 - - + -
355Z LEU* 5.5 1.3 - - + -
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Residues in contact with ASN 159 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155Z LEU 2.9 16.6 + - - +
156Z ALA* 3.6 6.7 - - - +
158Z LEU* 1.3 77.3 - - - +
160Z LYS* 1.3 63.1 + - - +
162Z GLY* 3.5 9.5 + - - -
164Z VAL* 3.4 24.5 + - - +
165Z GLN* 3.5 23.2 + - - +
166Z ALA* 3.8 7.5 - - - +
167Z ILE* 4.0 16.1 - - + +
178Z GLY 4.8 0.2 - - - +
179Z CYS* 3.5 3.9 - - - -
180Z LYS* 2.5 49.4 + - - +
181Z LYS 4.3 3.3 - - - +
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Residues in contact with LYS 160 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156Z ALA* 2.9 23.9 + - + +
157Z TYR* 4.1 4.3 - - + +
159Z ASN* 1.3 76.6 - - - +
161Z ALA* 1.3 63.0 + - - +
162Z GLY* 3.2 0.6 + - - -
177Z PHE 3.8 14.5 + - - +
178Z GLY 3.3 30.7 - - - +
180Z LYS* 4.7 18.0 + - - +
212Z GLU* 4.0 13.6 + - - -
298Z LEU* 4.2 10.7 - - + +
299Z ASN* 2.5 43.1 + - - +
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Residues in contact with ALA 161 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157Z TYR* 2.8 43.5 + - + +
159Z ASN 3.3 0.2 - - - -
160Z LYS* 1.3 78.6 - - - +
162Z GLY* 1.3 59.3 + - - +
163Z ILE* 3.3 21.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il